## [1] "Max fold diff lib size = 1.75956241223834"

## [1] "57820 total transcripts. Keeping 17782 transcripts after filtering"

QC checks

Heirarchical clustering

Heirarchical clustering based on expression profile Spearman correlations. This shows that the data are overall high quality (no outliers), with good grouping of samples within-cell lines. The biggest difference is clearly between colon and ovarian cell lines.

Multi-dimensional scaling

PCA

lCPM distributions

Comparing distribution of log-counts per million per sample looks reasonable

Replicate correlations

Comparing BIRC6 expression levels

Collapse replicates

Save LCPM data (rep collapsed)

Diff expression analysis

Collapse across replicates by summing read counts Model cell line as random effect

DE in BIRC6 Dependent lines

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GSEA

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## [1] "Running gene-permutation testing with 100000 perms"

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DE in BIRC6 Independent lines

GSEA

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Comparison of DE in Dependent vs Independent lines

Estimated KO effect in Dependent - Independent lines

GSEA

## [1] "Running gene-permutation testing with 100000 perms"

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Average DE across all cell lines

GSEA

## [1] "Running gene-permutation testing with 100000 perms"

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## [1] "Running gene-permutation testing with 100000 perms"

model individual cell line effects

GSEA

## [1] "Running gene-permutation testing with 100000 perms"
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